#------------------------------------------------------------------------------
#$Date: 2024-04-11 05:02:57 +0300 (Thu, 11 Apr 2024) $
#$Revision: 291175 $
#$URL: file:///home/coder/svn-repositories/cod/cif/2/31/24/2312470.cif $
#------------------------------------------------------------------------------
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/. The original data for this entry
# were provided by IUCr Journals, http://journals.iucr.org/.
#
# The file may be used within the scientific community so long as
# proper attribution is given to the journal article from which the
# data were obtained.
#
data_2312470
loop_
_publ_author_name
'Decato, Daniel'
'Palatinus, Lukáš'
'Stierle, Andrea'
'Stierle, Donald'
_publ_section_title
;
 Absolute structure determination of Berkecoumarin by X-ray and electron
 diffraction.
;
_journal_coeditor_code           YP3233
_journal_issue                   5
_journal_name_full
'Acta crystallographica. Section C, Structural chemistry'
_journal_paper_doi               10.1107/S2053229624003061
_journal_volume                  80
_journal_year                    2024
_chemical_absolute_configuration ad
_chemical_formula_iupac          'C13 H14 O5'
_chemical_formula_moiety         'C13 H14 O5'
_chemical_formula_sum            'C13 H14 O5'
_chemical_formula_weight         250.24
_chemical_name_common
;
Berkecoumarin
;
_chemical_name_systematic
;
(S)-8-Hydroxy-3-(2-hydroxypropyl)-6-methoxy-2H-chromen-2-one
;
_space_group_crystal_system      orthorhombic
_space_group_IT_number           19
_space_group_name_Hall           'P 2ac 2ab'
_space_group_name_H-M_alt        'P 21 21 21'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   4.9524(2)
_cell_length_b                   11.0302(4)
_cell_length_c                   20.9007(7)
_cell_measurement_reflns_used    7488
_cell_measurement_temperature    100
_cell_measurement_theta_max      57.679
_cell_measurement_theta_min      4.231
_cell_volume                     1141.72(7)
_computing_cell_refinement
;
SAINT (Bruker, 2015)
;
_computing_data_collection
;
APEX4 (Bruker, 2021)
;
_computing_data_reduction
;
SAINT (Bruker, 2015)
;
_computing_molecular_graphics
;
OLEX2 (Dolomanov et al.,  2009)
;
_computing_publication_material
;
OLEX2 (Dolomanov et al.,  2009)
;
_computing_structure_refinement
;
SHELXL2019 (Sheldrick, 2015a)
;
_computing_structure_solution
;
SHELXT2018 (Sheldrick, 2015b)
;
_diffrn_ambient_temperature      100
_diffrn_detector                 'Bruker Photon-100 area detector'
_diffrn_detector_area_resol_mean 10.5
_diffrn_measured_fraction_theta_full 0.991
_diffrn_measured_fraction_theta_max 0.991
_diffrn_measurement_device       'Fixed Chi three-circle'
_diffrn_measurement_device_type  'Bruker D8 VENTURE Duo'
_diffrn_measurement_method       'ω and φ scans'
_diffrn_radiation_monochromator  'Double Bounce Multilayer Mirror'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0531
_diffrn_reflns_av_unetI/netI     0.0353
_diffrn_reflns_limit_h_max       5
_diffrn_reflns_limit_h_min       -5
_diffrn_reflns_limit_k_max       10
_diffrn_reflns_limit_k_min       -12
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -22
_diffrn_reflns_number            9121
_diffrn_reflns_theta_full        57.822
_diffrn_reflns_theta_max         57.822
_diffrn_reflns_theta_min         4.230
_diffrn_source                   'microfocus sealed X-ray tube'
_diffrn_source_current           1.0
_diffrn_source_power             0.05
_diffrn_source_voltage           50.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.945
_exptl_absorpt_correction_T_max  0.7514
_exptl_absorpt_correction_T_min  0.5473
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
(SADABS; Krause et al.,  2015)
;
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.456
_exptl_crystal_description       needle
_exptl_crystal_F_000             528
_exptl_crystal_size_max          0.54
_exptl_crystal_size_mid          0.04
_exptl_crystal_size_min          0.02
_refine_diff_density_max         0.138
_refine_diff_density_min         -0.200
_refine_ls_abs_structure_details
;
Flack x determined using 555 quotients [(I+)-(I-)]/[(I+)+(I-)]
(Parsons et al., 2013)
;
_refine_ls_abs_structure_Flack   0.01(11)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.065
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     173
_refine_ls_number_reflns         1575
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.065
_refine_ls_R_factor_all          0.0322
_refine_ls_R_factor_gt           0.0272
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[σ²(Fo²)+(0.0336P)²+0.1948P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0639
_refine_ls_wR_factor_ref         0.0671
_reflns_number_gt                1463
_reflns_number_total             1575
_reflns_threshold_expression     'I > 2σ(I)'
_cod_data_source_file            yp3233.cif
_cod_data_source_block           I
_cod_database_code               2312470
_shelx_space_group_comment
;
The symmetry employed for this shelxl refinement is uniquely defined
by the following loop, which should always be used as a source of
symmetry information in preference to the above space-group names.
They are only intended as comments.
;
_shelx_estimated_absorpt_t_min   0.629
_shelx_estimated_absorpt_t_max   0.981
loop_
_space_group_symop_operation_xyz
'x, y, z'
'-x+1/2, -y, z+1/2'
'-x, y+1/2, -z+1/2'
'x+1/2, -y+1/2, -z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_calc_flag
_atom_site_occupancy
_atom_site_disorder_assembly
_atom_site_disorder_group
O O1 -0.0901(3) 0.68560(16) 0.53504(8) 0.0208(5) Uani d 1 . .
O O2 0.9293(4) 0.89438(16) 0.77962(8) 0.0206(5) Uani d 1 . .
O O3 0.2545(4) 1.03245(16) 0.64010(10) 0.0223(5) Uani d 1 . .
H H3 0.193(8) 1.011(3) 0.602(2) 0.075(14) Uiso d 1 . .
O O4 0.1590(3) 0.80255(15) 0.59658(8) 0.0177(5) Uani d 1 . .
O O5 0.5982(4) 0.48285(17) 0.48453(9) 0.0199(5) Uani d 1 . .
H H5 0.678(8) 0.553(4) 0.5006(19) 0.087(15) Uiso d 1 . .
C C1 0.1003(5) 0.6908(2) 0.57172(12) 0.0174(6) Uani d 1 . .
C C2 0.2688(5) 0.5891(2) 0.59160(12) 0.0166(6) Uani d 1 . .
C C3 0.4620(5) 0.6062(2) 0.63590(13) 0.0176(6) Uani d 1 . .
H H3A 0.566858 0.538836 0.649420 0.021 Uiso calc 1 . .
C C4 0.5149(5) 0.7233(2) 0.66349(12) 0.0161(6) Uani d 1 . .
C C5 0.7124(5) 0.7443(2) 0.71054(12) 0.0171(6) Uani d 1 . .
H H5A 0.818838 0.679459 0.726600 0.021 Uiso calc 1 . .
C C6 0.7489(5) 0.8616(2) 0.73308(13) 0.0172(6) Uani d 1 . .
C C7 0.5964(5) 0.9571(2) 0.70827(12) 0.0188(6) Uani d 1 . .
H H7 0.627148 1.037060 0.723494 0.023 Uiso calc 1 . .
C C8 0.4029(5) 0.9379(2) 0.66229(12) 0.0164(6) Uani d 1 . .
C C9 0.3617(5) 0.8193(2) 0.64084(13) 0.0168(6) Uani d 1 . .
C C10 0.2179(5) 0.4709(2) 0.55813(12) 0.0183(6) Uani d 1 . .
H H10A 0.022496 0.452254 0.559819 0.022 Uiso calc 1 . .
H H10B 0.315241 0.405419 0.580856 0.022 Uiso calc 1 . .
C C11 0.3097(5) 0.4737(3) 0.48815(13) 0.0176(6) Uani d 1 . .
H H11 0.226567 0.545180 0.466251 0.021 Uiso calc 1 . .
C C12 0.2325(5) 0.3592(2) 0.45283(13) 0.0212(6) Uani d 1 . .
H H12A 0.287804 0.365924 0.407951 0.032 Uiso calc 1 . .
H H12B 0.036456 0.347856 0.455119 0.032 Uiso calc 1 . .
H H12C 0.323150 0.289612 0.472531 0.032 Uiso calc 1 . .
C C13 1.0813(5) 0.7985(2) 0.80812(13) 0.0224(7) Uani d 1 . .
H H13A 1.195986 0.760465 0.775614 0.034 Uiso calc 1 . .
H H13B 0.957553 0.737936 0.825908 0.034 Uiso calc 1 . .
H H13C 1.194728 0.831385 0.842411 0.034 Uiso calc 1 . .
loop_
_atom_type_symbol
_atom_type_description
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C C 0.0181 0.0091 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
O O 0.0492 0.0322 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
loop_
_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle_site_symmetry_1
_geom_angle_site_symmetry_3
_geom_angle
_geom_angle_publ_flag
C6 O2 C13 . . 116.4(2) ?
C8 O3 H3 . . 107(3) ?
C1 O4 C9 . . 122.0(2) ?
C11 O5 H5 . . 118(3) ?
O1 C1 O4 . . 116.5(2) ?
O1 C1 C2 . . 125.9(2) ?
O4 C1 C2 . . 117.6(2) ?
C1 C2 C10 . . 116.0(2) ?
C3 C2 C1 . . 119.7(2) ?
C3 C2 C10 . . 124.2(2) ?
C2 C3 H3A . . 118.9 ?
C2 C3 C4 . . 122.1(2) ?
C4 C3 H3A . . 118.9 ?
C5 C4 C3 . . 123.7(2) ?
C9 C4 C3 . . 116.7(2) ?
C9 C4 C5 . . 119.6(2) ?
C4 C5 H5A . . 120.6 ?
C6 C5 C4 . . 118.8(2) ?
C6 C5 H5A . . 120.6 ?
O2 C6 C5 . . 124.9(2) ?
O2 C6 C7 . . 114.7(2) ?
C5 C6 C7 . . 120.4(2) ?
C6 C7 H7 . . 119.3 ?
C8 C7 C6 . . 121.4(3) ?
C8 C7 H7 . . 119.3 ?
O3 C8 C7 . . 119.9(2) ?
O3 C8 C9 . . 122.0(2) ?
C7 C8 C9 . . 118.1(2) ?
O4 C9 C4 . . 121.7(2) ?
O4 C9 C8 . . 116.6(2) ?
C4 C9 C8 . . 121.7(2) ?
C2 C10 H10A . . 109.2 ?
C2 C10 H10B . . 109.2 ?
C2 C10 C11 . . 112.2(2) ?
H10A C10 H10B . . 107.9 ?
C11 C10 H10A . . 109.2 ?
C11 C10 H10B . . 109.2 ?
O5 C11 C10 . . 110.3(2) ?
O5 C11 H11 . . 109.3 ?
O5 C11 C12 . . 106.5(2) ?
C10 C11 H11 . . 109.3 ?
C12 C11 C10 . . 112.0(2) ?
C12 C11 H11 . . 109.3 ?
C11 C12 H12A . . 109.5 ?
C11 C12 H12B . . 109.5 ?
C11 C12 H12C . . 109.5 ?
H12A C12 H12B . . 109.5 ?
H12A C12 H12C . . 109.5 ?
H12B C12 H12C . . 109.5 ?
O2 C13 H13A . . 109.5 ?
O2 C13 H13B . . 109.5 ?
O2 C13 H13C . . 109.5 ?
H13A C13 H13B . . 109.5 ?
H13A C13 H13C . . 109.5 ?
H13B C13 H13C . . 109.5 ?
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_site_symmetry_2
_geom_bond_distance
_geom_bond_publ_flag
O1 C1 . 1.217(3) ?
O2 C6 . 1.369(3) ?
O2 C13 . 1.428(3) ?
O3 H3 . 0.88(4) ?
O3 C8 . 1.358(3) ?
O4 C1 . 1.369(3) ?
O4 C9 . 1.378(3) ?
O5 H5 . 0.93(4) ?
O5 C11 . 1.434(3) ?
C1 C2 . 1.459(4) ?
C2 C3 . 1.344(4) ?
C2 C10 . 1.501(4) ?
C3 H3A . 0.9500 ?
C3 C4 . 1.439(4) ?
C4 C5 . 1.406(3) ?
C4 C9 . 1.386(4) ?
C5 H5A . 0.9500 ?
C5 C6 . 1.389(4) ?
C6 C7 . 1.396(4) ?
C7 H7 . 0.9500 ?
C7 C8 . 1.374(4) ?
C8 C9 . 1.397(4) ?
C10 H10A . 0.9900 ?
C10 H10B . 0.9900 ?
C10 C11 . 1.532(4) ?
C11 H11 . 1.0000 ?
C11 C12 . 1.512(4) ?
C12 H12A . 0.9800 ?
C12 H12B . 0.9800 ?
C12 H12C . 0.9800 ?
C13 H13A . 0.9800 ?
C13 H13B . 0.9800 ?
C13 H13C . 0.9800 ?
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_site_symmetry_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbond_publ_flag
O3 H3 O5 4_466 0.88(4) 1.87(4) 2.723(3) 161(4) yes
O5 H5 O1 1_655 0.93(4) 2.00(4) 2.915(3) 170(4) yes
loop_
_geom_torsion_atom_site_label_1
_geom_torsion_atom_site_label_2
_geom_torsion_atom_site_label_3
_geom_torsion_atom_site_label_4
_geom_torsion_site_symmetry_1
_geom_torsion_site_symmetry_2
_geom_torsion_site_symmetry_3
_geom_torsion_site_symmetry_4
_geom_torsion
_geom_torsion_publ_flag
O1 C1 C2 C3 . . . . -175.5(2) ?
O1 C1 C2 C10 . . . . 6.7(4) ?
O2 C6 C7 C8 . . . . -178.5(2) ?
O3 C8 C9 O4 . . . . -1.0(4) ?
O3 C8 C9 C4 . . . . 179.7(2) ?
O4 C1 C2 C3 . . . . 4.1(4) ?
O4 C1 C2 C10 . . . . -173.7(2) ?
C1 O4 C9 C4 . . . . -1.1(3) ?
C1 O4 C9 C8 . . . . 179.6(2) ?
C1 C2 C3 C4 . . . . -1.9(4) ?
C1 C2 C10 C11 . . . . 70.1(3) ?
C2 C3 C4 C5 . . . . 179.1(2) ?
C2 C3 C4 C9 . . . . -1.8(4) ?
C2 C10 C11 O5 . . . . 67.3(3) ?
C2 C10 C11 C12 . . . . -174.2(2) ?
C3 C2 C10 C11 . . . . -107.6(3) ?
C3 C4 C5 C6 . . . . 179.0(2) ?
C3 C4 C9 O4 . . . . 3.3(3) ?
C3 C4 C9 C8 . . . . -177.4(2) ?
C4 C5 C6 O2 . . . . 178.5(2) ?
C4 C5 C6 C7 . . . . -1.5(4) ?
C5 C4 C9 O4 . . . . -177.5(2) ?
C5 C4 C9 C8 . . . . 1.7(4) ?
C5 C6 C7 C8 . . . . 1.5(4) ?
C6 C7 C8 O3 . . . . 178.7(2) ?
C6 C7 C8 C9 . . . . 0.1(4) ?
C7 C8 C9 O4 . . . . 177.5(2) ?
C7 C8 C9 C4 . . . . -1.7(4) ?
C9 O4 C1 O1 . . . . 177.0(2) ?
C9 O4 C1 C2 . . . . -2.7(3) ?
C9 C4 C5 C6 . . . . -0.1(3) ?
C10 C2 C3 C4 . . . . 175.7(2) ?
C13 O2 C6 C5 . . . . -2.6(4) ?
C13 O2 C6 C7 . . . . 177.5(2) ?
